Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007706.1 Corchorus capsularis cultivar CVL-1 contig07727, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 31339
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:4267 original size:16 final size:16
Alignment explanation
Indices: 4234--4281 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
4224 AGCTGTCATT
* *
4234 TTTTTTATTTTTTTTCA
1 TTTTTTA-TGTTTCTCA
4251 TTTTTTATGTTTCTCA
1 TTTTTTATGTTTCTCA
*
4267 TTTTTTCTGTTTCTC
1 TTTTTTATGTTTCTC
4282 TAGAGGATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 21 0.75
17 7 0.25
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.75
Consensus pattern (16 bp):
TTTTTTATGTTTCTCA
Found at i:5504 original size:27 final size:26
Alignment explanation
Indices: 5473--5545 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
5463 AAGTGGACTT
5473 AAAATGACCAAAATGCCCCTGAATA-TGC
1 AAAATGACCAAAATGCCCCT---TAGTGC
*
5501 -AAATGACCAGAATG-CCCTTAGTGC
1 AAAATGACCAAAATGCCCCTTAGTGC
5525 AAAAATGACCAAAATGCCCCT
1 -AAAATGACCAAAATGCCCCT
5546 ATGTGACCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
23 2 0.05
24 3 0.08
26 17 0.44
27 17 0.44
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCCTTAGTGC
Found at i:13392 original size:85 final size:85
Alignment explanation
Indices: 13249--13419 Score: 333
Period size: 85 Copynumber: 2.0 Consensus size: 85
13239 AACGAGAAAT
13249 TACCCATTGTTACAAAGGATTTTATTTTACAATAGATCGCGTATATATAAATTTAGTGAAAAGCT
1 TACCCATTGTTACAAAGGATTTTATTTTACAATAGATCGCGTATATATAAATTTAGTGAAAAGCT
*
13314 GCTCGGGTTGGGAAGAGCGG
66 GCTCGGGCTGGGAAGAGCGG
13334 TACCCATTGTTACAAAGGATTTTATTTTACAATAGATCGCGTATATATAAATTTAGTGAAAAGCT
1 TACCCATTGTTACAAAGGATTTTATTTTACAATAGATCGCGTATATATAAATTTAGTGAAAAGCT
13399 GCTCGGGCTGGGAAGAGCGG
66 GCTCGGGCTGGGAAGAGCGG
13419 T
1 T
13420 GATGATCAGA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (85 bp):
TACCCATTGTTACAAAGGATTTTATTTTACAATAGATCGCGTATATATAAATTTAGTGAAAAGCT
GCTCGGGCTGGGAAGAGCGG
Found at i:15454 original size:6 final size:6
Alignment explanation
Indices: 15443--15469 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
15433 AAAATCTATA
15443 TATCTT TATCTT TATCTT TATCTT TAT
1 TATCTT TATCTT TATCTT TATCTT TAT
15470 ATTATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.67
Consensus pattern (6 bp):
TATCTT
Found at i:20083 original size:5 final size:5
Alignment explanation
Indices: 20073--20112 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
20063 AATGGTATAT
20073 AAATA AAATA AAATA AAATA AAATA AAATAA AAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA AAAT
20113 CATGGGTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:21273 original size:6 final size:6
Alignment explanation
Indices: 21259--21308 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
21249 AAAATTAACA
* *
21259 AAAACAC AAAAAC AAACAC AAAAAC AAAATAC GAAAAAT AAAAAC AAAAA
1 AAAA-AC AAAAAC AAAAAC AAAAAC AAAA-AC -AAAAAC AAAAAC AAAAA
21309 TAAAGAAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 26 0.70
7 7 0.19
8 4 0.11
ACGTcount: A:0.78, C:0.16, G:0.02, T:0.04
Consensus pattern (6 bp):
AAAAAC
Found at i:21302 original size:21 final size:21
Alignment explanation
Indices: 21278--21317 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
21268 AAACAAACAC
*
21278 AAAAACAAAAT-ACGAAAAAT
1 AAAAACAAAATAAAGAAAAAT
21298 AAAAACAAAAATAAAGAAAA
1 AAAAAC-AAAATAAAGAAAA
21318 GTAACAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAACAAAATAAAGAAAAAT
Found at i:23142 original size:18 final size:18
Alignment explanation
Indices: 23121--23155 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23111 AGAGGTTTTG
* *
23121 GTAGAGGTAATTTTGATT
1 GTAGAGGCAACTTTGATT
23139 GTAGAGGCAACTTTGAT
1 GTAGAGGCAACTTTGAT
23156 CGAAAAGGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.37
Consensus pattern (18 bp):
GTAGAGGCAACTTTGATT
Found at i:27772 original size:27 final size:26
Alignment explanation
Indices: 27685--27772 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 26
27675 ACTATTTTGT
*
27685 TTCATGAGTGTTATGATTTGCTCTAA
1 TTCATGAATGTTATGATTTGCTCTAA
* * * * * *
27711 TCTCATAATATTTTAATGTTTTGGTATTGA
1 T-TCATGA-ATGTT-ATGATTTGCT-CTAA
27741 TTCATGAATGTTATGATTTGCTCTAA
1 TTCATGAATGTTATGATTTGCTCTAA
27767 TGTCAT
1 T-TCAT
27773 AATATTTTGG
Statistics
Matches: 44, Mismatches: 13, Indels: 9
0.67 0.20 0.14
Matches are distributed among these distances:
26 4 0.09
27 17 0.39
28 7 0.16
29 13 0.30
30 3 0.07
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (26 bp):
TTCATGAATGTTATGATTTGCTCTAA
Found at i:27963 original size:17 final size:17
Alignment explanation
Indices: 27915--27964 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
27905 AAAAGAGTAC
27915 AATCCTCAAGAAGGAAA
1 AATCCTCAAGAAGGAAA
* **
27932 AAT-C-C-GGTGGGAAA
1 AATCCTCAAGAAGGAAA
27946 AATCCTCAAGAAGGAAA
1 AATCCTCAAGAAGGAAA
27963 AA
1 AA
27965 GAGTACACCC
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
14 9 0.38
15 2 0.08
16 2 0.08
17 11 0.46
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (17 bp):
AATCCTCAAGAAGGAAA
Found at i:30401 original size:41 final size:40
Alignment explanation
Indices: 30343--30582 Score: 205
Period size: 41 Copynumber: 5.7 Consensus size: 40
30333 AAGTTGCCCT
*
30343 TGTGTTATAATTGTGCTTAGGGACTTT-AGTTTAGATGCCTC
1 TGTGTTATAATTGTGCTT-GGGACTTTGA-TATAGATGCCTC
* *
30384 TGTGTTATAAATT-TGCTTGAGGACTTTGAAATAGGGATGCCCC
1 TGTGTTAT-AATTGTGCTTG-GGACTTTGATATA--GATGCCTC
30427 TGTGTTATAATTGTGCTTGGGGACTTTGATATAGATGCCTC
1 TGTGTTATAATTGTGCTT-GGGACTTTGATATAGATGCCTC
* * * * *
30468 TGTGTTGTAAATGTGTTTGAGGACTTTTGAAATAGAGAATTGCCCC
1 TGTGTTATAATTGTGCTTG-GGAC-TTTG--ATATAG-A-TGCCTC
** * *
30514 TGTGTTATAATTGTATTTGGGGACTTTGATGTAGATGTCTC
1 TGTGTTATAATTGTGCTT-GGGACTTTGATATAGATGCCTC
* *
30555 TGTGTTATAAATGTGATTGAGGACTTTG
1 TGTGTTATAATTGTGCTTG-GGACTTTG
30583 TAAGTAGAGT
Statistics
Matches: 164, Mismatches: 20, Indels: 30
0.77 0.09 0.14
Matches are distributed among these distances:
40 3 0.02
41 75 0.46
42 14 0.09
43 36 0.22
44 6 0.04
45 5 0.03
46 24 0.15
47 1 0.01
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.41
Consensus pattern (40 bp):
TGTGTTATAATTGTGCTTGGGACTTTGATATAGATGCCTC
Found at i:30434 original size:43 final size:42
Alignment explanation
Indices: 30376--30610 Score: 190
Period size: 41 Copynumber: 5.5 Consensus size: 42
30366 CTTTAGTTTA
*
30376 GATGCCTCTGTGTTATAAATTTGCTTGAGGACTTTGAAATAGG
1 GATGCCCCTGTGTTATAAATTTGCTTGAGGACTTTGAAATA-G
* *
30419 GATGCCCCTGTGTTAT-AATTGTGCTTGGGGACTTTGATATA-
1 GATGCCCCTGTGTTATAAATT-TGCTTGAGGACTTTGAAATAG
* * * *
30460 GATGCCTCTGTGTTGTAAATGTGTTTGAGGACTTTTGAAATAG
1 GATGCCCCTGTGTTATAAATTTGCTTGAGGAC-TTTGAAATAG
** * **
30503 AGAATTGCCCCTGTGTTAT-AATTGTATTTGGGGACTTTGATGTA-
1 -G-A-TGCCCCTGTGTTATAAATT-TGCTTGAGGACTTTGAAATAG
* * * * *
30547 GATGTCTCTGTGTTATAAATGTGATTGAGGACTTTGTAAGTAG
1 GATGCCCCTGTGTTATAAATTTGCTTGAGGACTTTG-AAATAG
* *
30590 AGTTGCCCCTGTGCTATAAAT
1 -GATGCCCCTGTGTTATAAAT
30611 GTATTTGGGG
Statistics
Matches: 153, Mismatches: 27, Indels: 23
0.75 0.13 0.11
Matches are distributed among these distances:
41 47 0.31
42 23 0.15
43 34 0.22
44 17 0.11
45 11 0.07
46 21 0.14
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (42 bp):
GATGCCCCTGTGTTATAAATTTGCTTGAGGACTTTGAAATAG
Found at i:30541 original size:87 final size:86
Alignment explanation
Indices: 30331--30626 Score: 368
Period size: 87 Copynumber: 3.5 Consensus size: 86
30321 TTTGCCATAT
* * * *
30331 AGAAGTTGCCCTTGTGTTATAATTGTGCTTAGGGACTTT-AGTTTAGATGCCTCTGTGTTATAAA
1 AGAA-TTGCCCCTGTGTTATAATTGTACTTGGGGACTTTGA-TATAGATGCCTCTGTGTTATAAA
* *
30395 TTTGCTTGAGGACTTTGAAATAG
64 TGTGATTGAGGACTTTGAAATAG
* * *
30418 -GGA-TGCCCCTGTGTTATAATTGTGCTTGGGGACTTTGATATAGATGCCTCTGTGTTGTAAATG
1 AGAATTGCCCCTGTGTTATAATTGTACTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATG
*
30481 TGTTTGAGGACTTTTGAAATAG
66 TGATTGAGGAC-TTTGAAATAG
* * *
30503 AGAATTGCCCCTGTGTTATAATTGTATTTGGGGACTTTGATGTAGATGTCTCTGTGTTATAAATG
1 AGAATTGCCCCTGTGTTATAATTGTACTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATG
*
30568 TGATTGAGGACTTTGTAAGTAG
66 TGATTGAGGACTTTG-AAATAG
* * *
30590 AG--TTGCCCCTGTGCTATAAATGTATTTGGGGACTTTG
1 AGAATTGCCCCTGTGTTATAATTGTACTTGGGGACTTTG
30627 GTTATTGGGT
Statistics
Matches: 187, Mismatches: 17, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
84 63 0.34
85 44 0.24
86 8 0.04
87 72 0.39
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (86 bp):
AGAATTGCCCCTGTGTTATAATTGTACTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATG
TGATTGAGGACTTTGAAATAG
Done.